I'm taking a class right now (Chemical Biology) in which we have to make a proposal as our end-of-the-quarter project. My proposal involves finding proteins that can bind to a particular carbohydrate displayed on certain cells in the body. The point is to generate molecular competition against a (protein) toxin made by a certain bacterium. The toxin is composed of two known parts, one of which binds to the carbohydrate on cells and the other which is the enzymatic payload.
Assuming I know/have the genetic sequence for the toxin, what are the logistics in using DNA shuffling/mutagenesis/ (any other technique that generates a large library of similar molecules) in order to make a large array of (similar to the toxin) proteins to test against the target carbohydrate-bearing cells? I know that making large libraries is a good way of directing searches for new molecules, but I am having trouble conceiving how, for example,
1. to MAKE all the proteins that correspond to all the varieties of DNA that I have generated
2. and to even affix all those proteins onto an array that allows me to run selections.